Mercurial > repos > lecorguille > xcms_retcor
changeset 3:3b44991a8e05 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
| author | lecorguille |
|---|---|
| date | Mon, 25 Apr 2016 11:14:51 -0400 |
| parents | 54cc3edfe35c |
| children | ac93ed26e4e1 |
| files | abims_xcms_retcor.xml planemo_test.sh test-data/faahKO.xset.group.RData test-data/faahKO_reduce.zip test-data/sacuri_dir_root.zip test-data/xset.group.RData |
| diffstat | 6 files changed, 38 insertions(+), 7 deletions(-) [+] |
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--- a/abims_xcms_retcor.xml Fri Apr 08 10:39:32 2016 -0400 +++ b/abims_xcms_retcor.xml Mon Apr 25 11:14:51 2016 -0400 @@ -99,7 +99,7 @@ </outputs> <tests> - <test> + <!--<test> <param name="image" value="xset.group.RData"/> <param name="methods|method" value="peakgroups"/> <param name="methods|smooth" value="loess"/> @@ -120,6 +120,28 @@ <has_text text="Sample classes: bio, blank" /> </assert_contents> </output> + </test>--> + <test> + <param name="image" value="faahKO.xset.group.RData"/> + <param name="methods|method" value="peakgroups"/> + <param name="methods|smooth" value="loess"/> + <param name="methods|extra" value="1"/> + <param name="methods|missing" value="1"/> + <param name="methods|options|option" value="show"/> + <param name="methods|options|span" value="0.2"/> + <param name="methods|options|family" value="gaussian"/> + <param name="methods|options|plottype" value="deviation"/> + <param name="zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <output name="log"> + <assert_contents> + <has_text text="object with 4 samples" /> + <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" /> + <has_text text="Mass range: 200.1-600 m/z" /> + <has_text text="Peaks: 9251 (about 2313 per sample)" /> + <has_text text="Peak Groups: 0" /> + <has_text text="Sample classes: KO, WT" /> + </assert_contents> + </output> </test> </tests>
--- a/planemo_test.sh Fri Apr 08 10:39:32 2016 -0400 +++ b/planemo_test.sh Mon Apr 25 11:14:51 2016 -0400 @@ -1,11 +1,10 @@ -planemo conda_init -planemo conda_install . -planemo test --install_galaxy --conda_dependency_resolution --galaxy_branch "dev" +# Example of planemo command to launch test -#All 1 test(s) executed passed. -#abims_xcms_retcor[0]: passed +# Note: --galaxy_branch "dev" is set to deal with zip file +# -- Use of installed package environments +# after having installing package on a local galaxy instance source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-xcms/1.44.0/lecorguille/package_bioconductor_xcms_1_44_0/0c38f7d43e08/env.sh planemo test --install_galaxy --galaxy_branch "dev" @@ -14,6 +13,16 @@ #abims_xcms_retcor[0]: passed +# -- Use of conda dependencies +planemo conda_init --conda_prefix /tmp/mc +planemo conda_install --conda_prefix /tmp/mc . +planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution --galaxy_branch "dev" + +#All 1 test(s) executed passed. +#abims_xcms_retcor[0]: passed + + +# -- Use of shed_test planemo shed_test --install_galaxy --galaxy_branch "dev" -t testtoolshed #All 1 test(s) executed passed. -#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/2.0.6[0]: passed \ No newline at end of file +#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/2.0.6[0]: passed